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- PDB-6kud: Crystal structure of Plasmodium falciparum histo-aspartic proteas... -

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Basic information

Entry
Database: PDB / ID: 6kud
TitleCrystal structure of Plasmodium falciparum histo-aspartic protease (HAP) zymogen (Form 3)
ComponentsHAP protein
KeywordsHYDROLASE / Histo-Aspartic protease / HAP / Plasmepsin / Proplasmepsin / Zymogen / Aspartic Protease
Function / homology
Function and homology information


plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / aspartic-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRathore, I. / Mishra, V. / Bhaumik, P.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (India)Ramalingaswami re-entry fellowship India
CitationJournal: Febs J. / Year: 2021
Title: Activation mechanism of plasmepsins, pepsin-like aspartic proteases from Plasmodium, follows a unique trans-activation pathway.
Authors: Rathore, I. / Mishra, V. / Patel, C. / Xiao, H. / Gustchina, A. / Wlodawer, A. / Yada, R.Y. / Bhaumik, P.
History
DepositionAug 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HAP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2333
Polymers43,0491
Non-polymers1842
Water48627
1
A: HAP protein
hetero molecules

A: HAP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4666
Polymers86,0982
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2490 Å2
ΔGint-16 kcal/mol
Surface area34090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.190, 69.910, 73.260
Angle α, β, γ (deg.)90.000, 125.710, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein HAP protein / Histo-aspartic protease


Mass: 43048.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: hap / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y006
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Lithium citrate tribasic tetrahydrate, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→29.19 Å / Num. obs: 11027 / % possible obs: 97.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.15
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1033

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0124refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.19 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.896 / SU B: 41.505 / SU ML: 0.344 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.4
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 552 5 %RANDOM
Rwork0.1843 ---
obs0.1876 10474 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 221.81 Å2 / Biso mean: 61.619 Å2 / Biso min: 18.98 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å20 Å2-0.57 Å2
2--2.46 Å2-0 Å2
3---0.39 Å2
Refinement stepCycle: final / Resolution: 2.9→29.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 12 27 3027
Biso mean--85.83 50.71 -
Num. residues----373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023071
X-RAY DIFFRACTIONr_bond_other_d0.0030.022904
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.9684153
X-RAY DIFFRACTIONr_angle_other_deg1.05336735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9965371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55825.515136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.82715544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.551154
X-RAY DIFFRACTIONr_chiral_restr0.1110.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213401
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02675
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 40 -
Rwork0.34 754 -
all-794 -
obs--97.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.4814-1.0463-0.73690.18040.11610.5980.05280.0982-0.24430.0298-0.02530.0724-0.06570.126-0.02750.3055-0.01490.06390.41110.00420.130346.554-5.8385.19
29.42556.91120.719911.74783.37611.39930.05090.38961.0581-1.2446-0.08980.1462-0.1917-0.24970.03891.0423-0.1470.31660.84860.26430.377245.478.941-0.507
32.47140.64721.530.70960.00232.6104-0.1864-0.02440.1492-0.18920.02080.1833-0.2187-0.16420.16560.22630.0749-0.05440.34250.00670.074320.5254.8254.242
42.6124-0.9152-0.44081.00830.82131.49290.03560.0717-0.0344-0.19710.0467-0.0317-0.26930.0468-0.08230.2755-0.0132-0.00960.404-0.01060.009141.8194.70415.845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 119P
2X-RAY DIFFRACTION2A120P - 10
3X-RAY DIFFRACTION3A11 - 218
4X-RAY DIFFRACTION4A219 - 328

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